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Re: [scipion-users] problem installing scipion3
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From: Pablo C. <pc...@cn...> - 2020-10-27 08:55:51
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I meant ls -l
/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em*
But I can see that environment lacks all scipion packages.
I'm guessing you do not have permission on the environment folder and
all goes to you HOME/.local installation.
If I'm right non of the plugins installation should work cause we do not
expect not having permissions on the environment.
Could you please verify this case?
ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages
Will list who owns that folder.
On 27/10/20 8:29, Moustafa, Ibrahim M. wrote:
> ls -l
> /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em
>
> gives nothing.
>
> The following packages exist in
> ls -l /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/
>
> brotli
> brotlipy-0.7.0-py3.8.egg-info
> certifi
> certifi-2020.6.20-py3.8.egg-info
> cffi
> cffi-1.14.3.dist-info
> _cffi_backend.cpython-38-x86_64-linux-gnu.so
> chardet
> chardet-3.0.4.dist-info
> cryptography
> cryptography-3.1.1.dist-info
> _distutils_hack
> distutils-precedence.pth
> easy_install.py
> idna
> idna-2.10.dist-info
> OpenSSL
> pip
> pip-20.2.4-py3.8.egg-info
> pkg_resources
> __pycache__
> pycparser
> pycparser-2.20.dist-info
> pyOpenSSL-19.1.0.dist-info
> PySocks-1.7.1.dist-info
> README.txt
> requests
> requests-2.24.0.dist-info
> SConse--(71%)
> scons-3.1.2-py3.8.egg-info
> setuptools
> setuptools-50.3.0.post20201006-py3.8.egg-info
> six-1.15.0.dist-info
> six.py
> sockshandler.py
> socks.py
> urllib3
> urllib3-1.25.11.dist-info
> wheel
> wheel-0.35.1-py3.6.egg-info
>
> Ibrahim
> ------------------------------------------------------------------------
> *From:* pc...@cn... <pc...@cn...>
> *Sent:* Tuesday, October 27, 2020 2:18 AM
> *To:* Mailing list for Scipion users <sci...@li...>
> *Subject:* Re: [scipion-users] problem installing scipion3
> What gives you:
>
> ls -l
> /usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_
> em_
>
> El 26 oct. 2020 17:57, "Moustafa, Ibrahim M." <ri...@ps...> escribió:
>
> Hi Pablo,
>
> Thanks for your reply.
>
> I tried your suggestions and I got the following error:
>
> ==================================================================================
> Scipion v3.0.5 () devel
> Building scipion-em-localrec ...
> /usr/local/miniconda/envs/.scipion3env/bin/python -m pip install
> scipion-em-localrec==3.0.1
> Collecting scipion-em-localrec==3.0.1
> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
> Installing collected packages: scipion-em-localrec
> Successfully installed scipion-em-localrec-3.0.1
> Traceback (most recent call last):
> File "/usr/local/scipion/pip/scipion/__main__.py", line 453, in
> <module>
> main()
> File "/usr/local/scipion/pip/scipion/__main__.py", line 296, in main
> installPluginMethods()
> File "/usr/local/scipion/pip/scipion/install/install_plugin.py",
> line 229, in installPluginMethod s
> installed = plugin.installPipModule(version=pluginVersion)
> File "/usr/local/scipion/pip/scipion/install/plugin_funcs.py",
> line 152, in installPipModule
> environment.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 748, in execute
> self._executeTargets(targetList)
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 690, in _executeTargets
> tgt.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 220, in execute
> command.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 160, in execute
> assert glob(t), ("target '%s' not built (after "
> AssertionError: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_
> em_localrec*' not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip in
> stall scipion-em-localrec==3.0.1')
> Error at main: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_e
> m_localrec*' not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip ins
> tall scipion-em-localrec==3.0.1')
>
> ==================================================================================
>
> Any idea to fix this?
>
> Thanks for help.
> Ibrahim
> ------------------------------------------------------------------------
> *From:* pc...@cn... <pc...@cn...>
> *Sent:* Saturday, October 24, 2020 11:56 PM
> *To:* Mailing list for Scipion users
> <sci...@li...>
> *Cc:* Carnegie, Mike Scott <mz...@ps...>
> *Subject:* Re: [scipion-users] problem installing scipion3
> Hi, I'm sorry about you poor experience installing the plugin
>
> Can you try:
>
> scipion3 python -m pip uninstall scipion-em-localrec
>
> And then:
>
> scipion3 installs -p scipion-em-localrec
>
> ?
> Then we can also check what is wrong with bumpy.
>
> All the best, Pablo.
>
> El 24 oct. 2020 2:12, "Moustafa, Ibrahim M." <ri...@ps...> escribió:
>
> Dear All,
>
> We are having so much trouble installing Scipion 3. We
> thought it went through installation but then it complained
> about xmipp because of conflict between numpy-1.19.1
> (installed with OpenCV) and numpy-1.18.4 (installed from pip).
> None of the plugins seem to be properly installed when we
> tried, although it showed "Successfully Finished' in the log!
>
> Trying to install localrec-em showed the following error:
>
> ===========================================================================================
> >scipion3 installp -p scipion-em-localrec
> /usr/local/miniconda/envs/.scipion3env/bin/python -m pip
> install scipion-em-localrec==3.0.1
> Collecting scipion-em-localrec==3.0.1
> Using cached scipion_em_localrec-3.0.1-py3-none-any.whl (530 kB)
> Installing collected packages: scipion-em-localrec
> Successfully installed scipion-em-localrec-3.0.1
> WARNING: Target directory
> /usr/local/scipion/pip/scipion_em_localrec-3.0.1.dist-info
> already exists. Specify --upgrade to force replacement.
> WARNING: Target directory /usr/local/scipion/pip/localrec
> already exists. Specify --upgrade to force replacement.
> Traceback (most recent call last):
> File "/usr/local/scipion/pip/scipion/__main__.py", line 453,
> in <module>
> main()
> File "/usr/local/scipion/pip/scipion/__main__.py", line 296,
> in main
> installPluginMethods()
> File
> "/usr/local/scipion/pip/scipion/install/install_plugin.py",
> line 229, in installPluginMethods
> installed = plugin.installPipModule(version=pluginVersion)
> File
> "/usr/local/scipion/pip/scipion/install/plugin_funcs.py", line
> 152, in installPipModule
> environment.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 748, in execute
> self._executeTargets(targetList)
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 690, in _executeTargets
> tgt.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 220, in execute
> command.execute()
> File "/usr/local/scipion/pip/scipion/install/funcs.py", line
> 160, in execute
> assert glob(t), ("target '%s' not built (after "
> AssertionError: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*'
> not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip
> install scipion-em-localrec==3.0.1')
> Error at main: target
> '/usr/local/miniconda/envs/.scipion3env/lib/python3.8/site-packages/scipion_em_localrec*'
> not built (after running
> '/usr/local/miniconda/envs/.scipion3env/bin/python -m pip
> install scipion-em-localrec==3.0.1')
> ==================================================================================
>
> Not sure what we are doing wrong! It would be appreciated
> if someone can share a "clear" protocol of how to properly
> install Scipion 3 along with plugins. We are mostly interested in
> localrec plugin.
>
> P.S. we are using py3.8 from miniconda
>
> Appreciate your help,
> Ibrahim
>
> Ibrahim M.Moustafa, Ph.D.
> Pennsylvania State University
> Biochemistry & Molecular Biology Dept.
> Millennium Science Complex
> University Park
> State College, PA16802
>
> Phone: (814) 863 5940
> Fax: (814) 865 7927
>
>
>
>
>
> _______________________________________________
> scipion-users mailing list
> sci...@li...
> https://lists.sourceforge.net/lists/listinfo/scipion-users
--
Pablo Conesa - *Madrid Scipion <http://scipion.i2pc.es> team*
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